Software for automated molecular dynamics exploration

C++ toolkit for post-processing molecular dynamics trajectories, with a focus on high-performance static and dynamic analyses of amorphous/glassy/polymer materials.

Building and analyzing residue interaction networks with cofactors (includes tutorial).

Structural analysis tools for OpenFE free energy calculations, built on MDAnalysis.

Efficiently compute off-resonance Raman spectra from first principles calculations (e.g. VASP) using polynomial models and machine learning..

Calculate lipid order parameters from Gromacs simulations

Gromacs Analysis Library for Rust

A Jekyll website for the research guides--UNIX, AMBER, Analysis, and R.

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

Order parameter calculations from Desmond Maestro .csv out files

Molecular Dynamics Trajectory Analysis Tools

CONAN is a tool to generate carbon and boron nitride structures, and to analyze molecular dynamics trajectories composed of a liquid at solid interfaces.

Library for Reading Gromacs TPR Files

A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan

A Python module for performing data analysis of atomistic trajectories relevant for glasses and supercooled liquids.

A package to find collective variables of dynamical systems by training neural networks

A package for multiple-scale simulations on the dynamical and kinetic processes in materials

Reactive molecular dynamics trajectory analysis

Center Any Group in a Gromacs Trajectory

"Atomic democracy" for site analysis of surfaces and bulks with known lattice structure(s).